How specific structural differences of Bcl2 proteins modulate the interaction with BH3 domains and apoptotic function

Intrinsic apoptosis is mainly regulated through a network of conserved interactions between Bcl-2 proteins involving hydrophobic binding grooves and BH3 domains. Despite these conserved interfaces, family members exhibit distinct binding affinities and play opposing roles in apoptosis. While static structural differences partially account for this divergence, it remains unclear how opposing apoptotic function reflects in BH3 helix engagement of individual members. Here, we investigate how a BidBH3 peptide engages with the hydrophobic groove of full-length membrane-anchored Bcl-xL and Bax to identify shared and unique features of binding that may relate to distinct apoptotic functions. Using state-of-the-art enhanced-sampling simulations, we mapped the complete binding and folding landscapes of these critical cell-death regulators in membranes. Our simulations align with experimental measurements in terms of predicted absolute binding affinities, and also capture the dynamic, atomistic details of the conformational changes induced by BH3 helices. Together, these details highlight the structural principles of BH3 in-groove engagement that determine apoptotic function, paving the way towards the modulation of the interactions among the Bcl-2 family members.